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Collecting Specimens in Outbreak Investigations. Goals. Define and describe animal and human clinical specimens. Define and describe environmental specimens such as food, water, and fomites. Discuss proper methods of human specimen collection and transportation .

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  • Define and describe animal and human clinical specimens.
  • Define and describe environmental specimens such as food, water, and fomites.
  • Discuss proper methods of human specimen collection and transportation
outbreaks involving clinical specimens
Outbreaks Involving Clinical Specimens
  • Human clinical specimens from case-patients
    • Blood
    • Serum
    • Urine
  • Type of specimen depends on the outbreak
  • Similar specimens from animals
  • Saliva
  • Hair
  • Feces
clinical specimen example 1 monkeypox
Clinical Specimen Example 1: Monkeypox
  • Midwestern United States: more than 70 individuals experienced febrile rash thought to be caused by monkeypox virus
    • Cases laboratory confirmed using blood, skin, lymph node, pharyngeal specimens
    • All lab-confirmed human cases associated with purchase of prairie dogs as pets
    • Samples from prairie dogs confirmed infection
    • Prairie dogs infected at animal distribution facility where housed/transported with exotic rodents from Africa
clinical specimen example 2 hantavirus
Clinical Specimen Example 2: Hantavirus
  • 1993, southwestern United States: outbreak of a fatal unexplained pulmonary illness associated with previously unknown type of hantavirus
    • Rodents found near homes of case-patients trapped and tested
    • Same strain of hantavirus cultured from tissue of a deer mouse captured near home of a case-patient who had died from the hantavirus strain
    • Results of a case-control study consistent with hypothesis that the fatal pulmonary disease was associated with proximity to infected deer mice.
outbreaks involving environmental specimens
Outbreaks Involving Environmental Specimens
  • Environmental specimens may be collected to confirm a source: food, water, fomites
    • Food/water samples often collected in food or waterborne outbreaks
    • Frequently collected in conjunction with human clinical samples
  • When clinical and environmental specimens yield same results, supports hypothesis that outbreak source is same as environmental specimen source
environmental specimen example 1 cholera
Environmental Specimen Example 1: Cholera
  • 1991, individual in Maryland tested positive for cholera while hospitalized for diarrhea and dehydration
    • Case-patient had not reported any common risk factors for cholera (raw shellfish, travel to foreign country, vaccination)
    • Attended party 2 days prior to hospitalization; other attendees also experienced diarrhea, had laboratory evidence of cholera
    • All case-patients reported eating homemade rice pudding prepared with frozen coconut milk imported from Thailand
    • Lab professionals cultured unopened packages of the same brand used to prepare the rice pudding
    • Tested positive for several types of Vibrio cholerae, Aeromonas, Salmonella
environmental specimen example 2 e coli
Environmental Specimen Example 2: E. coli
  • 1998, more than 50 cases of Escherichia coli 0157:H7were laboratory confirmed in Wisconsin
    • Case-control found association with consumption of fresh cheese curds produced by a particular cheese factory
    • Cheese samples from opened package of curds served at a party attended by several case-patients tested positive for E. coli 0157:H7
    • Pulsed-field gel electrophoresis demonstrated that 42 of the 44 case-patient isolates were indistinguishable from the curd isolates and from each other
    • Batch of unpasteurized cheddar cheese inadvertently used to make fresh cheese curds and incorrectly sold as pasteurized cheese curds
environmental specimen example 3 e coli
Environmental Specimen Example 3: E. coli
  • 1993, widespread outbreak of acute watery diarrhea occurred among 403,000 residents of Milwaukee, WI
    • Performed laboratory tests for enteric pathogens, examined ice made during time of the outbreak for cryptosporidium oocyst
    • Surveyed residents with confirmed or probable cryptosporidium infections
    • Outbreak caused by cryptosporidium oocysts that passed through filtration system of city's water-treatment plant
environmental specimen example 4 anthrax
Environmental Specimen Example 4: Anthrax
  • Anthrax investigation, 2001
    • Sampling of envelopes containing white powder confirmed suspicion of anthrax attack
    • Results from sampling of envelopes, postal facilities, clothing, news media offices, residences, and other sites used to evaluate presence and extent of anthrax contamination and guide decontamination process
challenges to detecting infectious agents in the environment
Challenges to Detecting Infectious Agents in the Environment
  • Infectious pathogens can be difficult to isolate and identify
  • Infectious enteric agents in water are particularly difficult to detect and quantify because concentration is more diluted than in clinical specimens
    • Only 13% of causative organisms of U.S. waterborne infectious disease outbreaks in 1991 and 1992 were identified
challenges to detecting infectious agents in the environment12
Challenges to Detecting Infectious Agents in the Environment
  • Some methods cannot determine viability or infectivity of the organisms
  • Identification of infectious agents in food also challenging because present in small quantities
  • Detection of infectious agents in both food and water may require costly specialized methods
    • 2004 survey of 56 state and territorial public health labs: 18% reported testing food specimens for viral pathogens
challenges to detecting infectious agents in the environment13
Challenges to Detecting Infectious Agents in the Environment
  • To ensure sample integrity and proper diagnosis and treatment, specimens need to be collected as quickly as possible once an outbreak is suspected
    • In a foodborne disease outbreak, the implicated food may be discarded or consumed in a matter of days
sampling onboard ship the vessel sanitation program
Sampling Onboard Ship: The Vessel Sanitation Program
  • Vessel Sanitation Program (VSP)
    • Jointly established by the CDC and cruise ship industry in 1970s
    • CDC inspects ships, performs surveillance of diarrheal illness, conducts outbreak investigations, offers sanitation training seminars to ship staff members
sampling onboard ship the vessel sanitation program15
Sampling Onboard Ship: The Vessel Sanitation Program
  • Epidemiological aspect: interviewing all crew members and passengers who are ill, collecting information (using standardized questionnaire) from all ship crew and passengers
  • Laboratory aspect: collection of stool, blood, vomitus from ill persons (as well as non-ill persons for comparison)
  • Environmental health aspect: examining and sampling potential outbreak sources such as on-board potable water, ice, food 
sampling onboard ship the vessel sanitation program16
Sampling Onboard Ship: The Vessel Sanitation Program
  • Investigated 21 acute gastroenteritis outbreaks in 2001
    • Stool samples revealed 9 outbreaks caused by noroviruses, 3 caused by bacteria, 9 of unknown etiology
    • Laboratory results shaped recommendations developed by CDC to stop outbreaks and prevent future outbreaks on cruise ships
pulsenet and dna fingerprinting
PulseNet and DNA “Fingerprinting”
  • PulseNet: national network by CDC
    • State and local health departments
    • Federal agencies such as CDC, USDA/FSIS, FDA
  • Perform standardized molecular subtyping of foodborne disease-causing bacteria using pulsed-field gel electrophoresis
  • Submit DNA “fingerprints” electronically to comprehensive database at CDC
    • Enables rapid comparison of patterns
    • Permits early identification of common source outbreaks
logistics of human clinical specimen collection and transportation
Logistics of Human Clinical Specimen Collection and Transportation
  • Most specimen collection during disease outbreak involves human clinical specimens
  • Laboratory confirmation of an etiologic agent is a ritical component of a successful outbreak investigation
    • Ability of a laboratory to successfully identify a pathogen depends on appropriate specimen collection and transportation
planning for human clinical specimen collection
Planning for Human Clinical Specimen Collection
  • Clinical and epidemiological data used to narrow range of possible causative agents
  • Clinical specimens needed to make a laboratory-confirmed diagnosis determined
  • Laboratory selected to perform testing and analysis
    • May be determined by the test(s) needed
planning for human clinical specimen collection20
Planning for Human Clinical Specimen Collection
  • Each lab has specific guidelines for specimen collection; all aspects should be discussed before collection begins
    • Sample type
    • Materials needed
    • Local or on-site processing
    • Transportation
    • Communication of results
planning for human clinical specimen collection21
Planning for Human Clinical Specimen Collection
  • Transportation details to discuss with lab
    • Timing and delivery of the collected samples
    • Required transport media
    • Transit route
    • Shipping requirements
    • Temperature requirements
    • Documentation
  • Packaging and transportation must comply with national regulations for transporting infectious material, should be reviewed with transport service
collecting human clinical specimens
Collecting Human Clinical Specimens
  • Specimens should be collected as soon as possible once an outbreak has been identified
    • Human specimens obtained early, particularly before antimicrobials are given to the patient, are more likely to yield the pathogen
  • In certain situations, specimen collection after a person recovers from illness may be equally important
    • Presence of antibodies in serum samples after recovery can confirm whether an individual’s illness or infection was related to the outbreak
collecting human clinical specimens23
Collecting Human Clinical Specimens
  • Before obtaining human clinical specimens, explain the purpose and procedure to the case-patient
  • Obtain an adequate amount of the specimen and handle with care
    • This may be the only opportunity to obtain a specimen during the outbreak
  • Sample must be collected properly to ensure that the pathogen or infectious agent can be recovered in a viable form
collecting human clinical specimens24
Collecting Human Clinical Specimens
  • Communication with the laboratory before specimen collection is critical to ensure appropriate collection technique, maintain the sample, and allow for proper diagnosis and treatment decisions
    • For example, not advisable to collect most fungal cultures with swabs because swab fibers can interfere with interpretation of results
    • Laboratory may reject the specimen for insufficient sample quantity or contamination from other body fluids
labeling and identification of human clinical specimens
Labeling and Identification of Human Clinical Specimens
  • Over 70% of information used to diagnose and treat a patient is derived from laboratory testing
  • Ensuring that specimens are accurately labeled at collection time is essential
    • Misidentification of a specimen leads to misidentification of a patient, can result in improper diagnosis and treatment
labeling and identification of human clinical specimens26
Labeling and Identification of Human Clinical Specimens
  • Laboratories may have different requirements
  • Labels affixed to the specimen container should include:
    • Patient’s name (first and last)
    • Unique identification number
    • Date, hour, place of collection
    • Type of sample
    • Specific anatomic culture site (to validate the specimen and help select appropriate medium)
    • Name of specimen collector
    • Specimens known to contain a dangerous pathogen should be clearly marked
labeling and identification of human clinical specimens27
Labeling and Identification of Human Clinical Specimens
  • Case investigation form with matching information should be completed for each specimen at time of collection, retained by investigation team for reference
  • All information should be printed legibly
storage and transport of human clinical specimens
Storage and Transport of Human Clinical Specimens
  • Specimens must be stored appropriately to preserve integrity
    • Environmental conditions can affect maintenance and survival
    • If they multiply or die during collection, transport, or storage, they no longer accurately represent the disease process 
  • Storage in appropriate medium and maintenance of proper temperature is critical
storage and transport of human clinical specimens29
Storage and Transport of Human Clinical Specimens
  • Requirements depend on type of specimen and sample, should be determined before specimen collection begins
  • Most specimens (exception of feces) need to be transported in sterile containers
    • Specimens transported in incorrect containers may be rejected by the lab
  • Specimen containers should be closed tightly
    • Labs may reject a specimen for signs of leakage or seepage, since this could expose laboratory personnel to contents 
storage and transport of human clinical specimens30
Storage and Transport of Human Clinical Specimens
  • Packaging must comply with postal and commercial regulations for transport of infectious materials
    • Regulations depend on type of transport (ground or air delivery)
    • Should be determined in consultation with lab and carrier prior to specimen collection
  • Receiving laboratory should be notified of pending shipment before transport
  • This issue touched on ways in which clinical and environmental specimens can provide valuable information to an outbreak investigation, and importance of appropriate and timely specimen collection
  • Next issues of FOCUS will discuss what happens after a specimen is sent to the lab and what types of laboratory diagnostics may be used to help identify an agent suspected in an outbreak
  • World Health Organization. Guidelines for the collection of clinical specimens during field investigations of outbreaks, 2000. surveillance/WHO_CDS_CSR_EDC_2000_4/en/
  • CDC. Guidelines for specimen collection. guide_sc.htm.
  • State health department websites
  • Centers for Disease Control and Prevention. Update: multistate outbreak of Monkeypox --- Illinois, Indiana, Kansas, Missouri, Ohio and Wisconsin, 2003. MMWR Morb Mort Wkly Rep. 2003; 52:642-626.
  • Centers for Disease Control and Prevention. All about hantaviruses. Available at: diseases/hanta/hps/noframes/outbreak.htm. Accessed December 12, 2006.
  • Centers for Disease Control and Prevention. Cholera associated with imported frozen coconut milk -— Maryland, 1991. MMWR Morb Mort Wkly Rep. 1991;40:844-845.
  • Centers for Disease Control and Prevention. Outbreak of Escherichia coli O157:H7 infection associated with eating fresh cheese curds --- Wisconsin, June 1998. MMWR Morb Mort Wkly Rep. 2000;41:911-913.
  • MacKenzie WR, Hoxie NJ, Proctor ME, et al. A massive outbreak in Milwaukee of cryptosporidium infection transmitted through the public water supply. N Engl J Med. 1994;331:161-167.
  • Jernigan DB, Raghunathan PL, Bell BP, et al. Investigation of bioterrorism-related anthrax, United States, 2001: Epidemiologic findings. Emerg Infect Dis. 2002;8:1019-1028.
  • Moe CL. Waterborne Transmission of infectious agents. In: Hurst CJ, Crawford RL, Knudsen GR, McInerney MJ, Stetzenbach LD, eds. Manual of Environmental Microbiology. 2nd ed. Washington, DC: ASM Press; 2002:136-152.
  • Majkowski J. Strategies for rapid response to emerging foodborne microbial hazards. Emerg Infect Dis. 1997;3:551-554.
  • Association of Public Health Laboratories. State Public Health Laboratory Food Safety Capacity, September 2004. Available at: Safety Issue Brief 9-14-04.pdf. Accessed December 12, 2006.
  • Miller, JM. A Guide to Specimen Management in Clinical Microbiology. 2nd ed. Washington, DC: ASM Press; 1996.
  • Dock, B. Improving accuracy of specimen labeling. Clin Lab Sci. 2005; 18:210.
  • Last JM, ed. A Dictionary of Epidemiology. 3rd ed. New York, NY: Oxford University Press, Inc.; 2001.
  • Kendrew J, ed. The Encyclopedia of Molecular Biology. Oxford, England: Blackwell Science; 1994.